1. Teleost fishes occupy a range of ecosystem and habitat types subject to large seasonal fluctuations. Temperate fishes in particular, survive large shifts in temperature, light availability, and access to certain habitats across seasons. Yet, there is limited understanding of how behavioral responses to a seasonally shifting environment might shape, or be shaped by, the nervous system. 2. Here we quantified variation in relative brain size and the size of five externally visible brain regions in a freshwater top predator, lake trout (Salvelinus namaycush), across six consecutive seasons in two different lakes. Acoustic telemetry data from one of our study lakes was collected during the study period from a different subset of individuals and used to infer relationships between brain size and seasonal behaviors (habitat use and movement rate). 3. Our results indicated that lake trout relative brain size was larger in the fall and winter compared to the spring and summer in both lakes. Larger brains coincided with increased use of nearshore lake habitats and increased horizontal movement rates by lake trout in the fall and winter based on acoustic telemetry. The telencephalon followed the same pattern as whole brain size, while the other brain regions (cerebellum, optic tectum, olfactory bulbs, hypothalamus) were only smaller in the spring. 4. Seasonal shifts in total brain size might reflect greater underlying changes in the size of the telencephalon. These findings provide evidence that flexibility in brain size could underpin shifts in behavior which could subserve functions associated with differential habitat use during cold and warm seasons and allow fish to succeed in seasonally variable temperate environments.